Changes in version 1.4.0 Versions on bioconductor and Github have been merged and, from now on, will have consistent version numbers. Changes in version 1.2.0 - Added two functions to handle ASCAT files instead of ChAS load_ascat and workflow_oncoscan.ascat. - Main workflow function workflow_oncoscan.run is renamed workflow_oncoscan.chas for consistency with the ASCAT function - Bug fixes in adjust_loh (crashed with segments of length 1 or if no LOH segments where present) - Bug fix in script run_oncoscan_workflow.R Changes in version 1.1.0 - To simplify the workflow, the gender of the patient is not taken into account anymore. That implies that in a male sample, a gain of 3 extra copies on the X or Y chromosome is considered as a gain and not an amplification anymore. For female samples, nothing changes. - The oncoscan coverage has been corrected to reflect only areas where there are groups of probes. Isolated probes where causing issues to identify arm-level alterations as ChAS segments where never extended to these probes and the 90% threshold could never be met (particularly on chromosomal arms 9p and Yq). - Minor corrections in vignette Changes in version 1.0.0 - The nLST test has been clinically validated on 384 patients from the PAOLA-1 trial and the recommended threshold is now >=15. - The default value for arm-level alterations has been set to 90% as mentioned in the publication [Christinat et al., J Mol Diagn 2021; PMID: 34454110]. - The genomic LOH score (percent of LOH bases) has been added; score_gloh. - Adds a flag "no tumor?" if the percentage of altered bases is less than 1%. - Package to be released on Bioconductor Changes in version 0.2.0 - Novel HRD score (nLST: number of LSTs, normalized by ploidy): score_nlst - Change in Oncoscan workflow to use the nLST score and thresholds. - New function to compute the number of Mb altered (with or without LOH): score_mbalt - New function to compute the average copy number: score_avgcn - New function to estimate the number of whole-genome duplication events (based on the average copy number and the thresholds defined by Carter et al.): score_estwgd